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- PDB-4wwr: Crystal Structure of Bag6-Ubl4A Dimerization Domain -

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Basic information

Entry
Database: PDB / ID: 4wwr
TitleCrystal Structure of Bag6-Ubl4A Dimerization Domain
Components
  • Large proline-rich protein BAG6
  • Ubiquitin-like protein 4A
KeywordsTRANSPORT PROTEIN / Endoplasmic Reticulum / Recombinant Proteins / Human
Function / homology
Function and homology information


BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / ubiquitin-like protein transferase activity / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding ...BAT3 complex / immune response-activating cell surface receptor signaling pathway / maintenance of unfolded protein / ubiquitin-like protein transferase activity / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / synaptonemal complex assembly / post-translational protein targeting to endoplasmic reticulum membrane / internal peptidyl-lysine acetylation / misfolded protein binding / natural killer cell activation / endoplasmic reticulum stress-induced pre-emptive quality control / : / ERAD pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / proteasome binding / ubiquitin-specific protease binding / regulation of embryonic development / polyubiquitin modification-dependent protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / : / Hsp70 protein binding / kidney development / proteasomal protein catabolic process / negative regulation of proteolysis / lung development / brain development / regulation of protein stability / protein modification process / ribosome binding / chromatin organization / ubiquitin-dependent protein catabolic process / protein-folding chaperone binding / spermatogenesis / cell differentiation / protein stabilization / signaling receptor binding / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. ...Ubl4, C-terminal TUGS domain / UBL4A-like, ubiquitin-like domain / Tethering Ubl4a to BAGS domain / Large proline-rich protein BAG6 / : / BCL2-associated athanogene 6 / Bag6, BAG-similar domain / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein 4A / Large proline-rich protein BAG6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMock, J.Y. / Chartron, J.W. / Clemons Jr., W.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097572 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Bag6 complex contains a minimal tail-anchor-targeting module and a mock BAG domain.
Authors: Mock, J.Y. / Chartron, J.W. / Zaslaver, M. / Xu, Y. / Ye, Y. / Clemons, W.M.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin-like protein 4A
A: Large proline-rich protein BAG6
H: Ubiquitin-like protein 4A
G: Large proline-rich protein BAG6
D: Ubiquitin-like protein 4A
C: Large proline-rich protein BAG6
F: Ubiquitin-like protein 4A
E: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)45,7408
Polymers45,7408
Non-polymers00
Water2,324129
1
B: Ubiquitin-like protein 4A
A: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)11,4352
Polymers11,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-21 kcal/mol
Surface area6490 Å2
MethodPISA
2
H: Ubiquitin-like protein 4A
G: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)11,4352
Polymers11,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-18 kcal/mol
Surface area6410 Å2
MethodPISA
3
D: Ubiquitin-like protein 4A
C: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)11,4352
Polymers11,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-20 kcal/mol
Surface area6210 Å2
MethodPISA
4
F: Ubiquitin-like protein 4A
E: Large proline-rich protein BAG6


Theoretical massNumber of molelcules
Total (without water)11,4352
Polymers11,4352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-25 kcal/mol
Surface area6520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.235, 56.494, 75.545
Angle α, β, γ (deg.)90.000, 96.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Ubiquitin-like protein 4A / Ubiquitin-like protein GDX


Mass: 5503.235 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL4A, DXS254E, GDX, UBL4 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / References: UniProt: P11441
#2: Protein
Large proline-rich protein BAG6 / BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG6 / HLA-B-associated ...BAG family molecular chaperone regulator 6 / BCL2-associated athanogene 6 / BAG6 / HLA-B-associated transcript 3 / Protein G3 / Protein Scythe


Mass: 5931.694 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG6, BAT3, G3 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / References: UniProt: P46379
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 298.13 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG-3350, 0.05 HEPES sodium pH 7.0, 1% tryptone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→19.65 Å / Num. obs: 26499 / % possible obs: 98.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 34.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.033 / Net I/σ(I): 13.9 / Num. measured all: 78055
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.0530.8131.7581919480.620.56598.2
8.94-19.652.80.01349.68182940.9990.0188.7

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.647 Å / FOM work R set: 0.7466 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1334 5.04 %
Rwork0.2245 25145 -
obs0.2267 26479 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 361.81 Å2 / Biso mean: 54.59 Å2 / Biso min: 17.31 Å2
Refinement stepCycle: final / Resolution: 2→19.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 0 129 3287
Biso mean---48.62 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073198
X-RAY DIFFRACTIONf_angle_d1.0724302
X-RAY DIFFRACTIONf_chiral_restr0.042494
X-RAY DIFFRACTIONf_plane_restr0.005563
X-RAY DIFFRACTIONf_dihedral_angle_d14.4321266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.07150.40711460.3312444259098
2.0715-2.15430.34831120.31592548266098
2.1543-2.25220.34791390.292460259998
2.2522-2.37080.37171230.27712522264599
2.3708-2.5190.30521490.26092470261999
2.519-2.71310.3711360.2672521265799
2.7131-2.98520.30231290.25322522265199
2.9852-3.41530.25951190.22992534265399
3.4153-4.29540.23571370.18752539267699
4.2954-19.64790.20061440.17732585272999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.39640.72-1.10713.972-0.22644.2446-0.11050.3726-0.5867-0.31220.0618-0.2020.3213-0.16450.15130.2362-0.08240.01140.212-0.05680.197623.5165-57.963817.6814
26.87282.3249-0.94962.3393-0.57641.05820.2449-0.45340.40740.0314-0.24450.1803-0.16190.00560.02610.2379-0.0205-0.00770.2331-0.03820.152616.5367-50.532221.0968
36.85130.37-1.94212.649-0.4754.8925-0.0050.60920.1099-0.6189-0.3343-0.0875-0.4635-0.1390.34070.3799-0.095-0.10340.32310.06040.255320.4702-50.197110.8819
47.21092.3145-5.12614.364-2.74566.5422-0.46080.3266-0.7406-0.13350.2488-0.08320.9783-0.19080.23780.2627-0.0910.00330.3315-0.04980.36958.8661-63.21522.5061
55.10791.3099-2.86161.2948-0.77562.587-0.16080.8193-0.0087-0.15120.0080.33110.1324-0.4438-0.24070.3736-0.0996-0.09630.36760.0060.520337.5581-88.368412.7435
61.9709-0.49780.74663.0412-1.15932.4291-0.1006-0.3694-0.08170.19110.23710.005-0.1074-0.2217-0.12440.2704-0.0363-0.02450.3390.00340.472130.9155-88.768619.8878
77.8693-2.1827-1.26563.8536-1.24471.77170.0749-0.6760.7570.53260.2333-0.3934-0.47490.146-0.2750.3302-0.0899-0.0160.3403-0.06810.553339.1315-83.718421.2024
83.7449-0.4964-0.80071.586-1.47096.71440.16651.811-0.7051-0.9205-0.3783-0.93450.6546-0.912-0.02010.4540.1810.06161.0778-0.18650.819422.0952-83.76998.9135
99.27741.94776.76332.5145-0.2596.14510.3809-0.3192-0.7413-0.3139-0.01850.6273-0.7092-0.7612-0.47040.55370.1557-0.04660.4822-0.16110.509439.0527-75.92084.2692
105.1172-1.59820.45913.0405-0.7276.2340.47830.1975-0.9564-0.3234-0.01010.13590.24710.0529-0.62510.48290.06960.030.3833-0.09490.44452.3143-80.6610.311
118.9301-2.30132.26212.41520.48741.13070.2931.46350.8211-0.7788-0.39280.4974-0.91520.47540.09481.01040.06290.03810.46420.00650.465545.3521-70.6377-1.5759
127.5965-0.8292-0.62857.89212.91896.695-0.1853-0.8010.4360.52680.76780.88180.69251.1397-0.46350.466-0.08420.04650.6957-0.10780.75957.9418-79.733914.0286
135.7802-2.4213.91566.5656-1.55566.72330.3758-0.34281.60430.3013-0.1342-0.3671-0.36960.5194-0.00760.3239-0.04370.05880.4482-0.09630.327727.6082-59.385133.6601
143.70841.4261-0.07222.1158-1.98632.59740.2246-1.6703-0.70230.477-0.228-0.0417-0.59210.74940.1660.4014-0.0702-0.07440.53020.05140.257634.9547-66.103536.3797
153.6207-1.0771-0.34172.9269-0.00512.6647-0.1879-0.343-0.60240.44830.09970.11330.1243-0.10070.10530.3286-0.04720.0450.38310.11460.28725.6819-69.423533.034
164.2445-1.45730.06595.4097-1.26750.35310.0902-1.03931.92610.2032-0.2755-0.3282-0.3781-0.0212-0.28020.3913-0.03130.05220.4280.01050.545141.9254-58.655227.362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1053:1071)A1053 - 1071
2X-RAY DIFFRACTION2(chain A and resid 1072:1105)A1072 - 1105
3X-RAY DIFFRACTION3(chain B and resid 93:123)B93 - 123
4X-RAY DIFFRACTION4(chain B and resid 124:138)B124 - 138
5X-RAY DIFFRACTION5(chain C and resid 1053:1070)C1053 - 1070
6X-RAY DIFFRACTION6(chain C and resid 1071:1105)C1071 - 1105
7X-RAY DIFFRACTION7(chain D and resid 94:127)D94 - 127
8X-RAY DIFFRACTION8(chain D and resid 128:139)D128 - 139
9X-RAY DIFFRACTION9(chain E and resid 1053:1077)E1053 - 1077
10X-RAY DIFFRACTION10(chain E and resid 1078:1103)E1078 - 1103
11X-RAY DIFFRACTION11(chain F and resid 94:128)F94 - 128
12X-RAY DIFFRACTION12(chain F and resid 129:138)F129 - 138
13X-RAY DIFFRACTION13(chain G and resid 1053:1070)G1053 - 1070
14X-RAY DIFFRACTION14(chain G and resid 1071:1105)G1071 - 1105
15X-RAY DIFFRACTION15(chain H and resid 94:123)H94 - 123
16X-RAY DIFFRACTION16(chain H and resid 124:138)H124 - 138

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